Research and Development


Combining the power of computation and experiments to improve research and technology development
We are a multidisciplinary group of scientists interested in understanding the fundamental Structure-Dynamics-Function relationship observed in biomolecules and the role their diversity plays in the mechanisms of complex biological processes through a robust Theoretical-Computational-Experimental approach. The biological models we use to study Biomolecular Diversity are viruses, antibiotics, proteins, and lipid membranes.
We use an integrative approach, leveraging methods and techniques from Molecular Biophysics, Multi-Scale Molecular Modeling, Molecular Dynamics, Bioinformatics, Molecular Biology, Structural Biology, High Performance Computing, Biotechnology and Genetic Engineering, Information Systems and Software Development.

Biomolecular Diversity Laboratory and Research Group


International Peer-Reviewed Scientific Publications


Innovative Software Developments


Students Graduated


Funded Research Projects


Awards Received


plus Citations
TOP-5 Most Cited

  1. (2009) VIPERdb2: An enhanced and web API enabled relational database for structural virology.
    Nucleic Acids Research . 37:D436-D442
    CV 10.1093/nar/gkn840 JCR IF 11.147
  2. (2003) A comparative study of the hydration of Na+ and K+ with refined polarizable model potentials.
    Journal of Chemical Physics . 118:7062-7073
    CV 10.1063/1.1559673 JCR IF 2.997
  3. (2005) Evidence for a mechanism by which w-3 polyunsaturated lipids may affect membrane protein function.
    Biochemistry . 44:10164-10169
    CV 10.1021/bi050822e JCR IF 2.952
  4. (2004) Minimalist molecular model for nanopore selectivity.
    Physical review letters . 93:168104
    CV 10.1103/PhysRevLett.93.168104 JCR IF 9.161
  5. (2006) Ion hydration in nanopores and the molecular basis of selectivity.
    Biophysical Chemistry . 124:243-250
    CV 10.1016/j.bpc.2006.04.012 JCR IF 2.352
Journal Covers

  1. (2018) CapsidMesh CV

  1. Immunomodulatory Effects of Allium sativum L. and its Constituents against Viral Infections and Metabolic Diseases.
    Current Topics in Medicinal Chemistry 22:109-131.
    CV 10.2174/1568026621666211122163156 JCR IF 3.218
  2. Differences in the local anesthesia effect by lidocaine and bupivacaine based on free energy analysis.
    Molecular Simulation 48:745-751.
    CV 10.1080/08927022.2022.2053118 JCR IF 2.178
  3. Líneas argumentativas de profesores de biología sobre el origen del coronavirus SARS-Cov-2
    Enseñanza de las Ciencias 40:71-88.
    CV 10.5565/rev/ensciencias.3537 JCR IF 1.183
  4. Experimental and theoretical insights into trans influence of organo-sulfur and -selenium ligands in 5,6-membered palladium(II) cationic pincer complexes based on iminophosphoranes.
    New Journal of Chemistry 46:9344-9356.
    CV 10.1039/D2NJ00924B JCR IF 3.591
  5. Viral capsid nanoindentation simulations using octree-type data structures.
    Mathematics and Computers in Simulation.
    CV 10.1016/j.matcom.2022.06.017 JCR IF 3.601
  6. Repurposing drugs as potential therapeutics for the SARS-Cov-2 viral infection: Automatizing a blind molecular docking high-throughput pipeline.
    Molecular Docking - Recent Advances. IntechOpen ISBN 978-1-80356-468-5.
    CV Accepted Book Chapter
  7. Computer Numerical Control Micromilling of a Microfluidic Acrylic Device With a Staggered Restriction for Magnetic Nanoparticle-Based Immunoassays.
    CV Accepted JCR IF
  8. ESX3 secretion system components of Mycobacterium tuberculosis are potential drug targets of the avermectin family.
    submitted .
    CV Under review JCR IF

  1. NAT2 polymorphisms associated with development of hepatoxicity after first-line tuberculosis treatment in Mexican patients: from genotype to molecular structure characterization.
    Clinica Chimica Acta 519:153-162.
    CV 10.1016/j.cca.2021.04.017 JCR IF 2.615
  2. Biotechnological Production of Biomaterials and Their Applications
    in PART 2: BIOMATERIALS AND BIOMOLECULES, Handbook of Research on Bioenergy and Biomaterials Consolidated and Green Processes , Apple Academic Press

  1. VIPERdb v3.0: a structure-based data analytics platform for viral capsids.
    Nucleic Acids Research 37:D436-D442.
    CV 10.1093/nar/gkaa1096 JCR IF 11.147
  2. Analyzing structural alterations of mitochondrial intermembrane space superoxide scavengers cytochrome-c and SOD1 after methylglyoxal treatment
    PLoS ONE 15:e0232408
    DOI 10.1371/journal.pone.0232408 JCR IF 2.776
    Open Access: Download

  1. Hot-spots and their contribution to the self-assembly of the viral capsid: in-silico prediction and analysis.
    International Journal of Molecular Sciences
    Special Issue "Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids"

    DOI 10.3390/ijms20235966 JCR IF 4.556
    Open Access: Download
  2. Hot-spots and their contribution to the self-assembly of the viral capsid: in-vitro validation.
    DOI Pre-print 10.1101/724146
  3. Parallel High-Performance Computing Algorithm to Generate FEM-Compliant Volumetric Mesh Representations of Biomolecules at Atomic Scale
    Supercomputing. Communications in Computer and Information Science. CCIS Book Chapter 1151:318-333 .
    CV 10.1007/978-3-030-38043-4_25

  1. VIPERdb: A Tool for Virus Research.
    Annual Review of Virology . 5:477-488
    CV 10.1146/annurev-virology-092917-043405 JCR IF 6.566
  2. CapsidMesh: atomic-detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties.
    International Journal for Numerical Methods in Biomedical Engineering . e2991
    CV 10.1002/cnm.2991 JCR IF 2.082
  3. HTMol: full-stack solution for remote access, visualization, and analysis of Molecular Dynamics trajectory data.
    Journal of Computer-Aided Molecular Design 32:869-876
    CV 10.1007/s10822-018-0141-y JCR IF 3.250
  4. Plant-based chimeric HPV-virus-like particles bearing amyloid-β epitopes elicit antibodies able to recognize amyloid plaques in APP-tg mouse and Alzheimer´s disease brains.
    Inflammopharmacology . 26:817-827
    CV 10.1007/s10787-017-0408-2 JCR IF 3.838

  1. A Multi-Phase Solvation Model for Biological Membranes: Molecular Action Mechanism of Amphotericin B.
    Journal of Chemical Theory and Computation . 13:3388–3397
    CV 10.1021/acs.jctc.7b00337 JCR IF 5.313
  2. Porcine circovirus type 2 protective epitope densely carried by chimeric papaya ringspot virus-like particles expressed in E. coli as a cost-effective vaccine manufacture alternative.
    Biotechnology and Applied Biochemistry . 64:406-414
    CV 10.1002/bab.1491 JCR IF 1.559
  3. Evolution of substrate specificity in a retained enzyme driven by gene loss.
    eLife eLife . 6:e22679
    CV 10.7554/eLife.22679 JCR IF 7.551

  1. Structure based sequence analysis of viral and cellular protein assemblies.
    Journal of Structural Biology . 196:299-308
    CV 10.1016/j.jsb.2016.07.013 JCR IF 3.754
  2. An Amphotericin B derivative equally potent to Amphotericin B and with increased safety.
    PloS One . 11:e0162171
    CV 10.1371/journal.pone.0162171 JCR IF 2.776
  3. Antagonism or synergism between Papaya ringspot virus and Papaya mosaic virus in Carica papaya is determined by their order of infection.
    Virology . 489:179-191
    CV 10.1016/j.virol.2015.11.026 JCR IF 2.657

  1. Highly efficient strategy for the heterologous expression and purification of soluble Cowpea chlorotic mottle virus capsid protein and in vitro pH-dependent assembly of virus-like particles.
    Journal of Virological Methods . 225:23-29
    CV 10.1016/j.jviromet.2015.08.023 JCR IF 1.746
  2. CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google maps.
    Journal of Structural Biology . 190:47-55
    CV 10.1016/j.jsb.2015.02.003 JCR IF 3.754
  3. Insights into the evolution of enzyme substrate promiscuity after the discovery of (beta alpha)8 isomerase evolutionary intermediates from a diverse metagenome.
    BMC Evolutionary Biology . 15:107-121
    CV 10.1186/s12862-015-0378-1 JCR IF 3.045

12 published peer-reviewed scientific papers

Technology Development

Methods, Protocols, Modeling, Visualization, and Analysis Tools for the Study of BioMolecular Diversity, Structural Biology and Biological BigData

Structural Virology

VIPERdb Science Gateway

Global Repository of Structural Virology: Viruses are the most abundant pathogens affecting all forms of life. A major component of a virus is a protein shell, known as the viral capsid, that encapsulates the genomic material. The capsid has the fundamental functions to protect and transport the viral genome, and recognize the host cell. VIPERdb is a database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools.

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Structural Virology

CapsidMaps & S-score

CapsidMaps is an interactive analysis and visualization tool. It facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity S-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application.

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Structural Virology


Descriptions of the capsid macromolecular complex have been proposed at different scales of approximation in the past, however, little is known about the physical properties of the capsid. CapsidMesh is a methodology to generate a structured volumetric mesh of icosahedral viral capsids based on their atomic information. The CapsidMesh models are suitable for numerical simulations and analysis of a physical process. We have used CapsidMesh to simulate the capsid nanoindentation of several viruses previously characterized by Atomic Force Microscopy experiments. Our results show that the atomic detail of the CapsidMesh is sufficient to reproduce anisotropic properties of the particle.

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Structural Bioinformatics


Next-generation Molecular Dynamics Web Visualization: HTMoL is a light-weight full-stack plugin-free application to display the three-dimensional structure and dynamics of biomolecules on any web browser. HTMoL can be used as a graphical interface to access MD data located at a high performance computing cluster where simulations are generated, or as supplementary documentation for scientific research publications as a way to readily share MD results.

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Molecular Modeling

MMPSM: Membrane Multi-Phase Solvation Model

We use a thermodynamic approach in which we represent the biological membrane by a multiphase solvation model with atomic detail and calculate the free energy of transferring a drug molecule between phases with different dielectric properties.

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AI-based 2D analysis of 'omics' derived data (e.g. microarrays, differential gene expression, etc.)
"The English-language neologism omics informally refers to a field of study in biology ending in -omics, such as genomics, proteomics or metabolomics. The related suffix -ome is used to address the objects of study of such fields, such as the genome, proteome or metabolome respectively. Omics aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms." Read more.

Coming soon
Structural Bioinformatics


The Molecular Dynamics database.
"Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules, and is thus a type of N-body simulation. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic evolution of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are calculated using interatomic potentials or molecular mechanics force fields. The method was originally developed within the field of theoretical physics in the late 1950s but is applied today mostly in chemical physics, materials science and the modelling of biomolecules." Read more.

Coming soon

Group Members

Research Team


  1. Armando Díaz Valle (2023)

Ph. D.

  1. Mayur Rambhau Dange (2025)
  2. Aldo Fernando Herrera Rodulfo (2024)


  1. Martha Susana García Delgado (2022)
  2. Ilse Alexandra Martínez Solís (2022)
  3. César Hernández Urquizu (2022)
  4. Leidy Alexandra Arévalo Rodríguez (2023)
  5. Mary Luz Gómez López (2023)
  6. Jesús Hernán Quijano Ibarra (2023)

Research Assistant

  1. Angélica Lizeth Toiber Estrella (since 01/2022)

Development Team

Tech. Assistant



  1. Prof. Charles Brooks III, University of Michigan
  2. Dr. Vijay S. Reddy, The Scripps Research Institute
  3. Dr. Chris Henry, Argonne National Laboratory
  4. Dr. Scott Feller, Wabash College


  1. Dr. Ali Tavassoli, University of Southampton


  1. Dra. Laura Silva Rosales, Departamento de Ingeniería Genética
  2. Dra. Tatiana Iveth Salazar López, Unidad Monterrey
  3. Dra. Roxana Gutiérrez Vidal, Unidad Monterrey
  4. Dr. Gonzalo Peñaloza Jiménez, Unidad Monterrey
  5. Dr. Miguel Gómez Lim, Departamento de Ingeniería Genética
  6. Dr. Amilcar Meneses Viveros, Departamento de Computación
  7. Dr. Francisco Barona Gómez, Unidad de Genómica Avanzada


  1. Dr. Iván Ortega Blake, Instituto de Ciencias Físicas
  2. Dr. Rubén Paul Gaytán Colin, Unidad de Síntesis y Secuenciación de ADN, Instituto de Biotecnología


  1. Dr. Salvador Botello Rionda, Departamento de Computación
  2. Dr. Rafael Herrera Guzmán, Departamento de Matemáticas Básicas


  1. Dr. José M. Falcón González, Unidad Profesional Interdisciplinaria de Ingeniería


  1. Dr. Abel Gutiérrez Ortega, Unidad de Biotecnología Médica y Farmacéutica


  1. Dra. Alcione García González, Fisicoquímica de Interfases, Facultad de Ciencias Químicas


  1. Dra. Beatriz Silva Ramirez, Centro de Investigación Biomédica del Noreste
  2. Dra. Katia Peñuelas Urquides, Centro de Investigación Biomédica del Noreste



  1. José M. Falcón González (2015)
  2. Mónica N. Jiménez García (2014)
  3. Alcione García González (2010)

Ph. D.

  1. Mariana Andrade Medina (2021)
  2. José L. Alonzo Velázquez (2017)
  3. Daniel J. Montiel García (2016)


  1. Natalia Carolina Valencia Vallejo (2021)
  2. Irwing David Vásquez Cerqueda (2021)
  3. Josué Alejandro Alemán Vilis (2020)
  4. Alejandra G. Valdéz Lara (2019)
  5. Raúl A. Galván Juárez (2019)
  6. Aldo A. Pérez Montoya (2019)
  7. A. Yarely de la Rosa González (2019)
  8. Omar I. Lara Ramirez (2016)
  9. Angélica A. Serrano Rubio (2015)
  10. Armando Díaz Valle (2014)
  11. Victor Villa Moreno (2013)
  12. Guillermo Amaro Rico (2013)
  13. Gabriela Chávez Calvillo (2012)


  1. Fernando Jasso (2020)
  2. Emmanuel Quijas Valades (2017)
  3. Julio C. González Vázquez (2017)
  4. Eduardo González Zavala (2017)
  5. José Cabello Zavala (2016)
  6. Eliot G. Cruz Ponce (2016)
  7. Leonardo Alvarez Rivera (2015)
  8. Francisco J. Becerra Toledo (2015)
  9. Adan Vega Ramírez (2015)
  10. Joel Chacón Castillo (2014)
  11. Oscar Ornelas Alvarado (2014)
  12. Miguel A. Ochoa Montes (2014)
  13. Ramiro Ramos Meléndes (2014)
  14. Francisco Aguilar Salas (2014)
  15. Adrián Benavides Rosales (2014)

Research Assistant

  1. Melissa González (2019)
  2. Luis Mario Zepeda Guzmán (2019)
  3. Claudia Cruz Belli (2018)
  4. J. Julian Santoyo Flores (2016)
  5. Gabriel Jiménez Domínguez (2016)
  6. Victor Villa Moreno (2014)
  7. Mariana Andrade Medina (2013)


Mauricio Carrillo-Tripp, Ph. D.

Principal Investigator
Unidad Monterrey



+52 811 156 1740 ext 4520